names.push_back(temp.getName());
database->addSequence(temp);
}
- database->generateDB();
+ if ((method == "kmer") && (!shortcuts)) {;} //don't print
+ else {database->generateDB(); }
}else if ((method == "kmer") && (!needToGenerate)) {
ifstream kmerFileTest(kmerDBName.c_str());
database->readKmerDB(kmerFileTest);
}
fastaFile.close();
- database->generateDB();
+ if ((method == "kmer") && (!shortcuts)) {;} //don't print
+ else {database->generateDB(); }
}else if ((method == "kmer") && (!needToGenerate)) {
ifstream kmerFileTest(kmerDBName.c_str());
}
/**************************************************************************************************/
+double Classify::getLogExpSum(vector<double> probabilities, int& maxIndex){
+ try {
+ // http://jblevins.org/notes/log-sum-exp
+
+ double maxProb = probabilities[0];
+ maxIndex = 0;
+
+ int numProbs = (int)probabilities.size();
+
+ for(int i=1;i<numProbs;i++){
+ if(probabilities[i] >= maxProb){
+ maxProb = probabilities[i];
+ maxIndex = i;
+ }
+ }
+
+ double probSum = 0.0000;
+
+ for(int i=0;i<numProbs;i++){
+ probSum += exp(probabilities[i] - maxProb);
+ }
+
+ probSum = log(probSum) + maxProb;
+
+ return probSum;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Classify", "getLogExpSum");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+